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Items: 48

1.

Whole genome shotgun phylogenomics resolves the pattern and timing of swallowtail butterfly evolution.

Allio R, Scornavacca C, Benoit N, Clamens AL, Sperling FAH, Condamine FL.

Syst Biol. 2019 May 7. pii: syz030. doi: 10.1093/sysbio/syz030. [Epub ahead of print]

PMID:
31062850
2.

Pervasive hybridizations in the history of wheat relatives.

Glémin S, Scornavacca C, Dainat J, Burgarella C, Viader V, Ardisson M, Sarah G, Santoni S, David J, Ranwez V.

Sci Adv. 2019 May 1;5(5):eaav9188. doi: 10.1126/sciadv.aav9188. eCollection 2019 May.

3.

Reconciling multiple genes trees via segmental duplications and losses.

Dondi R, Lafond M, Scornavacca C.

Algorithms Mol Biol. 2019 Mar 20;14:7. doi: 10.1186/s13015-019-0139-6. eCollection 2019.

4.

Generation of level-k LGT Networks.

Pons JC, Scornavacca C, Cardona G.

IEEE/ACM Trans Comput Biol Bioinform. 2019 Jan 25. doi: 10.1109/TCBB.2019.2895344. [Epub ahead of print]

PMID:
30703035
5.

OrthoMaM v10: Scaling-Up Orthologous Coding Sequence and Exon Alignments with More than One Hundred Mammalian Genomes.

Scornavacca C, Belkhir K, Lopez J, Dernat R, Delsuc F, Douzery EJP, Ranwez V.

Mol Biol Evol. 2019 Apr 1;36(4):861-862. doi: 10.1093/molbev/msz015.

6.

A phylogenetic framework of the legume genus Aeschynomene for comparative genetic analysis of the Nod-dependent and Nod-independent symbioses.

Brottier L, Chaintreuil C, Simion P, Scornavacca C, Rivallan R, Mournet P, Moulin L, Lewis GP, Fardoux J, Brown SC, Gomez-Pacheco M, Bourges M, Hervouet C, Gueye M, Duponnois R, Ramanankierana H, Randriambanona H, Vandrot H, Zabaleta M, DasGupta M, D'Hont A, Giraud E, Arrighi JF.

BMC Plant Biol. 2018 Dec 5;18(1):333. doi: 10.1186/s12870-018-1567-z.

7.

Finding a most parsimonious or likely tree in a network with respect to an alignment.

Kelk S, Pardi F, Scornavacca C, van Iersel L.

J Math Biol. 2019 Jan;78(1-2):527-547. doi: 10.1007/s00285-018-1282-2. Epub 2018 Aug 19.

8.

Exploring the Tiers of Rooted Phylogenetic Network Space Using Tail Moves.

Janssen R, Jones M, Erdős PL, van Iersel L, Scornavacca C.

Bull Math Biol. 2018 Aug;80(8):2177-2208. doi: 10.1007/s11538-018-0452-0. Epub 2018 Jun 14.

9.

RecPhyloXML: a format for reconciled gene trees.

Duchemin W, Gence G, Arigon Chifolleau AM, Arvestad L, Bansal MS, Berry V, Boussau B, Chevenet F, Comte N, Davín AA, Dessimoz C, Dylus D, Hasic D, Mallo D, Planel R, Posada D, Scornavacca C, Szöllosi G, Zhang L, Tannier É, Daubin V.

Bioinformatics. 2018 Nov 1;34(21):3646-3652. doi: 10.1093/bioinformatics/bty389.

10.

Improved Maximum Parsimony Models for Phylogenetic Networks.

Van Iersel L, Jones M, Scornavacca C.

Syst Biol. 2018 May 1;67(3):518-542. doi: 10.1093/sysbio/syx094.

PMID:
29272537
11.

ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets.

Brozovic M, Dantec C, Dardaillon J, Dauga D, Faure E, Gineste M, Louis A, Naville M, Nitta KR, Piette J, Reeves W, Scornavacca C, Simion P, Vincentelli R, Bellec M, Aicha SB, Fagotto M, Guéroult-Bellone M, Haeussler M, Jacox E, Lowe EK, Mendez M, Roberge A, Stolfi A, Yokomori R, Brown CT, Cambillau C, Christiaen L, Delsuc F, Douzery E, Dumollard R, Kusakabe T, Nakai K, Nishida H, Satou Y, Swalla B, Veeman M, Volff JN, Lemaire P.

Nucleic Acids Res. 2018 Jan 4;46(D1):D718-D725. doi: 10.1093/nar/gkx1108.

12.

Inferring incomplete lineage sorting, duplications, transfers and losses with reconciliations.

Chan YB, Ranwez V, Scornavacca C.

J Theor Biol. 2017 Nov 7;432:1-13. doi: 10.1016/j.jtbi.2017.08.008. Epub 2017 Aug 9.

PMID:
28801222
13.

Rearrangement moves on rooted phylogenetic networks.

Gambette P, van Iersel L, Jones M, Lafond M, Pardi F, Scornavacca C.

PLoS Comput Biol. 2017 Aug 1;13(8):e1005611. doi: 10.1371/journal.pcbi.1005611. eCollection 2017 Aug.

14.

DeCoSTAR: Reconstructing the Ancestral Organization of Genes or Genomes Using Reconciled Phylogenies.

Duchemin W, Anselmetti Y, Patterson M, Ponty Y, Bérard S, Chauve C, Scornavacca C, Daubin V, Tannier E.

Genome Biol Evol. 2017 May 1;9(5):1312-1319. doi: 10.1093/gbe/evx069.

15.

Efficient FPT Algorithms for (Strict) Compatibility of Unrooted Phylogenetic Trees.

Baste J, Paul C, Sau I, Scornavacca C.

Bull Math Biol. 2017 Apr;79(4):920-938. doi: 10.1007/s11538-017-0260-y. Epub 2017 Feb 28.

PMID:
28247121
16.

On the consistency of orthology relationships.

Jones M, Paul C, Scornavacca C.

BMC Bioinformatics. 2016 Nov 11;17(Suppl 14):416. doi: 10.1186/s12859-016-1267-3.

17.

Incomplete Lineage Sorting in Mammalian Phylogenomics.

Scornavacca C, Galtier N.

Syst Biol. 2017 Jan 1;66(1):112-120. doi: 10.1093/sysbio/syw082.

PMID:
28173480
18.

Fast algorithm for the reconciliation of gene trees and LGT networks.

Scornavacca C, Mayol JCP, Cardona G.

J Theor Biol. 2017 Apr 7;418:129-137. doi: 10.1016/j.jtbi.2017.01.024. Epub 2017 Jan 20.

PMID:
28111320
19.

Resolution and reconciliation of non-binary gene trees with transfers, duplications and losses.

Jacox E, Weller M, Tannier E, Scornavacca C.

Bioinformatics. 2017 Apr 1;33(7):980-987. doi: 10.1093/bioinformatics/btw778.

PMID:
28073758
20.

Do Branch Lengths Help to Locate a Tree in a Phylogenetic Network?

Gambette P, van Iersel L, Kelk S, Pardi F, Scornavacca C.

Bull Math Biol. 2016 Sep;78(9):1773-1795. Epub 2016 Sep 22.

PMID:
27659024
21.

On the fixed parameter tractability of agreement-based phylogenetic distances.

Bordewich M, Scornavacca C, Tokac N, Weller M.

J Math Biol. 2017 Jan;74(1-2):239-257. doi: 10.1007/s00285-016-1023-3. Epub 2016 May 25.

PMID:
27221239
22.

ecceTERA: comprehensive gene tree-species tree reconciliation using parsimony.

Jacox E, Chauve C, Szöllősi GJ, Ponty Y, Scornavacca C.

Bioinformatics. 2016 Jul 1;32(13):2056-8. doi: 10.1093/bioinformatics/btw105. Epub 2016 Feb 26.

PMID:
27153713
23.

A Resolution of the Static Formulation Question for the Problem of Computing the History Bound.

Matsieva J, Kelk S, Scornavacca C, Whidden C, Gusfield D.

IEEE/ACM Trans Comput Biol Bioinform. 2017 Mar-Apr;14(2):404-417. doi: 10.1109/TCBB.2016.2527645. Epub 2016 Feb 11.

PMID:
26887004
24.

Fast and accurate branch lengths estimation for phylogenomic trees.

Binet M, Gascuel O, Scornavacca C, Douzery EJ, Pardi F.

BMC Bioinformatics. 2016 Jan 7;17:23. doi: 10.1186/s12859-015-0821-8.

25.

A fast method for calculating reliable event supports in tree reconciliations via Pareto optimality.

To TH, Jacox E, Ranwez V, Scornavacca C.

BMC Bioinformatics. 2015 Nov 14;16:384. doi: 10.1186/s12859-015-0803-x.

26.

SylvX: a viewer for phylogenetic tree reconciliations.

Chevenet F, Doyon JP, Scornavacca C, Jacox E, Jousselin E, Berry V.

Bioinformatics. 2016 Feb 15;32(4):608-10. doi: 10.1093/bioinformatics/btv625. Epub 2015 Oct 29.

PMID:
26515823
27.

Efficient algorithms for reconciling gene trees and species networks via duplication and loss events.

To TH, Scornavacca C.

BMC Genomics. 2015;16 Suppl 10:S6. doi: 10.1186/1471-2164-16-S10-S6. Epub 2015 Oct 2.

28.

ANISEED 2015: a digital framework for the comparative developmental biology of ascidians.

Brozovic M, Martin C, Dantec C, Dauga D, Mendez M, Simion P, Percher M, Laporte B, Scornavacca C, Di Gregorio A, Fujiwara S, Gineste M, Lowe EK, Piette J, Racioppi C, Ristoratore F, Sasakura Y, Takatori N, Brown TC, Delsuc F, Douzery E, Gissi C, McDougall A, Nishida H, Sawada H, Swalla BJ, Yasuo H, Lemaire P.

Nucleic Acids Res. 2016 Jan 4;44(D1):D808-18. doi: 10.1093/nar/gkv966. Epub 2015 Sep 29.

29.

Inferring gene duplications, transfers and losses can be done in a discrete framework.

Ranwez V, Scornavacca C, Doyon JP, Berry V.

J Math Biol. 2016 Jun;72(7):1811-44. doi: 10.1007/s00285-015-0930-z. Epub 2015 Sep 4.

PMID:
26337177
30.

Reconstructible phylogenetic networks: do not distinguish the indistinguishable.

Pardi F, Scornavacca C.

PLoS Comput Biol. 2015 Apr 7;11(4):e1004135. doi: 10.1371/journal.pcbi.1004135. eCollection 2015 Apr. Erratum in: PLoS Comput Biol. 2019 Jun 14;15(6):e1007137.

31.

Exploring the space of gene/species reconciliations with transfers.

Chan YB, Ranwez V, Scornavacca C.

J Math Biol. 2015 Nov;71(5):1179-209. doi: 10.1007/s00285-014-0851-2. Epub 2014 Dec 14.

PMID:
25502987
32.

Joint amalgamation of most parsimonious reconciled gene trees.

Scornavacca C, Jacox E, Szöllősi GJ.

Bioinformatics. 2015 Mar 15;31(6):841-8. doi: 10.1093/bioinformatics/btu728. Epub 2014 Nov 6.

33.

A practical approximation algorithm for solving massive instances of hybridization number for binary and nonbinary trees.

van Iersel L, Kelk S, Lekić N, Scornavacca C.

BMC Bioinformatics. 2014 May 5;15:127. doi: 10.1186/1471-2105-15-127.

34.

OrthoMaM v8: a database of orthologous exons and coding sequences for comparative genomics in mammals.

Douzery EJ, Scornavacca C, Romiguier J, Belkhir K, Galtier N, Delsuc F, Ranwez V.

Mol Biol Evol. 2014 Jul;31(7):1923-8. doi: 10.1093/molbev/msu132. Epub 2014 Apr 9.

PMID:
24723423
35.

Reconciliation-based detection of co-evolving gene families.

Chan YB, Ranwez V, Scornavacca C.

BMC Bioinformatics. 2013 Nov 20;14:332. doi: 10.1186/1471-2105-14-332.

36.

Support measures to estimate the reliability of evolutionary events predicted by reconciliation methods.

Nguyen TH, Ranwez V, Berry V, Scornavacca C.

PLoS One. 2013 Oct 4;8(10):e73667. doi: 10.1371/journal.pone.0073667. eCollection 2013.

37.

Bio++: efficient extensible libraries and tools for computational molecular evolution.

Guéguen L, Gaillard S, Boussau B, Gouy M, Groussin M, Rochette NC, Bigot T, Fournier D, Pouyet F, Cahais V, Bernard A, Scornavacca C, Nabholz B, Haudry A, Dachary L, Galtier N, Belkhir K, Dutheil JY.

Mol Biol Evol. 2013 Aug;30(8):1745-50. doi: 10.1093/molbev/mst097. Epub 2013 May 21.

PMID:
23699471
38.

Representing a set of reconciliations in a compact way.

Scornavacca C, Paprotny W, Berry V, Ranwez V.

J Bioinform Comput Biol. 2013 Apr;11(2):1250025. doi: 10.1142/S0219720012500254. Epub 2012 Dec 28.

PMID:
23600816
39.

A first step toward computing all hybridization networks for two rooted binary phylogenetic trees.

Scornavacca C, Linz S, Albrecht B.

J Comput Biol. 2012 Nov;19(11):1227-42. doi: 10.1089/cmb.2012.0192.

PMID:
23134319
40.

Dendroscope 3: an interactive tool for rooted phylogenetic trees and networks.

Huson DH, Scornavacca C.

Syst Biol. 2012 Dec 1;61(6):1061-7. doi: 10.1093/sysbio/sys062. Epub 2012 Jul 10.

PMID:
22780991
41.

Fast computation of minimum hybridization networks.

Albrecht B, Scornavacca C, Cenci A, Huson DH.

Bioinformatics. 2012 Jan 15;28(2):191-7. doi: 10.1093/bioinformatics/btr618. Epub 2011 Nov 9.

PMID:
22072387
42.

On the elusiveness of clusters.

Kelk SM, Scornavacca C, van Iersel L.

IEEE/ACM Trans Comput Biol Bioinform. 2012;9(2):517-34. doi: 10.1109/TCBB.2011.128. Epub 2011 Sep 27.

PMID:
21968961
43.

Multigenic phylogeny and analysis of tree incongruences in Triticeae (Poaceae).

Escobar JS, Scornavacca C, Cenci A, Guilhaumon C, Santoni S, Douzery EJ, Ranwez V, Glémin S, David J.

BMC Evol Biol. 2011 Jun 24;11:181. doi: 10.1186/1471-2148-11-181.

44.

Tanglegrams for rooted phylogenetic trees and networks.

Scornavacca C, Zickmann F, Huson DH.

Bioinformatics. 2011 Jul 1;27(13):i248-56. doi: 10.1093/bioinformatics/btr210.

45.

A survey of combinatorial methods for phylogenetic networks.

Huson DH, Scornavacca C.

Genome Biol Evol. 2011;3:23-35. doi: 10.1093/gbe/evq077. Epub 2010 Nov 15.

46.

PhySIC_IST: cleaning source trees to infer more informative supertrees.

Scornavacca C, Berry V, Lefort V, Douzery EJ, Ranwez V.

BMC Bioinformatics. 2008 Oct 4;9:413. doi: 10.1186/1471-2105-9-413.

47.

Exploring the solution space of sorting by reversals, with experiments and an application to evolution.

Braga MD, Sagot MF, Scornavacca C, Tannier E.

IEEE/ACM Trans Comput Biol Bioinform. 2008 Jul-Sep;5(3):348-56. doi: 10.1109/TCBB.2008.16.

PMID:
18670039
48.

PhySIC: a veto supertree method with desirable properties.

Ranwez V, Berry V, Criscuolo A, Fabre PH, Guillemot S, Scornavacca C, Douzery EJ.

Syst Biol. 2007 Oct;56(5):798-817.

PMID:
17918032

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